Hi all,
I just tried, a couple of days ago, the CONV_LOOP = 1 option in the
full_analysis,py script.
Strangely (as opposed to Douglas), it works well for me with different
DIFF_MODEL options. Also, I get the same exact results for differents
rounds of calculation/optimization (chi-squared, model convergence,
etc).
I used line 1.2 revision 3354.
Cheers
Séb
Douglas Kojetin wrote:
Hi Edward,
I am just picking back up on my relaxation analysis, and noticed that
the CONV_LOOP = 1 function is full_analysis.py does not seem to work
properly. I get the following error:
"""
#####################
# Convergence tests #
#####################
Chi-squared test:
chi2 (k-1): 164.3021658998544
chi2 (k): 168.91097779838205
The chi-squared value has not converged.
Identical model-free models test:
Traceback (most recent call last):
File "/opt/relax/1.2/relax", line 454, in ?
Relax()
File "/opt/relax/1.2/relax", line 166, in __init__
self.interpreter.run()
File "/opt/relax/1.2/prompt/interpreter.py", line 213, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/opt/relax/1.2/prompt/interpreter.py", line 388, in run_script
console.interact(intro, local, script_file, quit)
File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
interact_script
execfile(script_file, local)
File "full_analysis.py", line 574, in ?
Main(self.relax)
File "full_analysis.py", line 247, in __init__
converged = self.convergence(run=name)
File "full_analysis.py", line 368, in convergence
curr_models = curr_models + self.relax.data.res[run][i].model
AttributeError: Element instance has no attribute 'model'
"""
Thanks,
Doug
On Jun 27, 2007, at 11:22 AM, Edward d'Auvergne wrote:
Hi,
To commit changes to the repository, you need to become a relax
developer. There is detailed information in the relax manual about
this long process. Alternatively if you run the command svn diff to
create a patch file, I can then apply the patch and make the commit
for you. In this case however I am making the changes to the 1.3
repository line and then back porting to the 1.2 line (this is the
origin of the relax_data_store error you saw before). Therefore if
you post what the changes are, I will manually apply them to 1.3 and
then back port to 1.2.
Cheers,
Edward
P.S. The change to line 290 was unnecessary as far as I can see (I
could be wrong though). And I also replaced the looping over
LOCAL_TM_MODELS and MF_MODELS with a single test within the model-free
model loop which already exists - just to simplify the code. The
changes have been committed to the repository.
On 6/27/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Another update. I had to change a few more lines, but the script
seems to work properly now.
% diff OLD.py NEW.py
229a230,231
> if name in self.relax.data.run_names:
> run.delete(name)
290a293,294
> if 'final' in self.relax.data.run_names:
> run.delete('final')
524a529,531
> for name_to_remove in LOCAL_TM_MODELS:
> if name_to_remove in self.relax.data.run_names:
> run.delete(name_to_remove)
526a534,536
> for name_to_remove in MF_MODELS:
> if name_to_remove in self.relax.data.run_names:
> run.delete(name_to_remove)
If you would like me to commit these changes, just let me know where
I can find instructions on how to do so.
Thanks,
Doug
On Jun 26, 2007, at 3:58 AM, Edward d'Auvergne wrote:
Whoops, that should have been 'self.relax.data.run_names'! It's
all
fixed in the repository.
Cheers,
Edward
On 6/25/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi Edward,
A new error, that appears before the first round of iteration
starts
after executing the script:
---------------------------------------------------------------------
---
----------------------------
Traceback (most recent call last):
File "/home/dkojetin/bin/relax", line 454, in ?
Relax()
File "/home/dkojetin/bin/relax", line 166, in __init__
self.interpreter.run()
File "/opt/relax/1.2/prompt/interpreter.py", line 213, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/opt/relax/1.2/prompt/interpreter.py", line 388, in
run_script
console.interact(intro, local, script_file, quit)
File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
interact_script
execfile(script_file, local)
File "n3.py", line 578, in ?
Main(self.relax)
File "n3.py", line 230, in __init__
self.load_tensor()
File "n3.py", line 499, in load_tensor
if 'previous' in self.relax.data.runs:
AttributeError: Data instance has no attribute 'runs'
Doug
On Jun 25, 2007, at 8:54 AM, Edward d'Auvergne wrote:
Hi,
Sorry, that relax_data_store was 1.3 line specific and I
forgot to
change that for the 1.2 line. The repository code should now
have
that fixed.
Cheers,
Edward
On 6/25/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hello,
Here is the error reported by the modified full_analysis.py
script
(named n.py in the below Traceback):
#--start
---------------------------------------------------------------------
---
----------------------------
Traceback (most recent call last):
File "/home/dkojetin/bin/relax", line 454, in ?
Relax()
File "/home/dkojetin/bin/relax", line 166, in __init__
self.interpreter.run()
File "/opt/relax/1.2/prompt/interpreter.py", line 213, in
run
run_script(intro=self.relax.intro_string,
local=self.local,
script_file=self.relax.script_file, quit=1)
File "/opt/relax/1.2/prompt/interpreter.py", line 388, in
run_script
console.interact(intro, local, script_file, quit)
File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
interact_script
execfile(script_file, local)
File "n.py", line 577, in ?
Main(self.relax)
File "n.py", line 229, in __init__
self.load_tensor()
File "n.py", line 498, in load_tensor
if relax_data_store.has_key('previous'):
NameError: global name 'relax_data_store' is not defined
#--end
Thanks,
Doug
On Jun 25, 2007, at 4:42 AM, Edward d'Auvergne wrote:
Hi,
I've just made modifications to the 1.2 and 1.3 repository
lines to
hopefully fix this problem. Could you try again to see if
the
script
works this time?
Cheers,
Edward
On 6/25/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx>
wrote:
Hi Edward,
I gave the new script a try, setting CONV_LOOP = 1, but it
reported
an error after optimizing the first round:
"""
Convergence:
[ No ]
relax> run.create(run='previous', run_type='mf')
RelaxError: The run 'previous' already exists.
"""
If you have any suggestions for changes to the script, send
them my
way and I'll give it a try.
Doug
On Jun 24, 2007, at 11:47 AM, Edward d'Auvergne wrote:
Hi,
The simplest way to do this would be to use a while loop
using a
modified version of the convergence() function which
returns
1 or 0
depending on whether the results have converged
(exactly like
your
suggestion). I have added this looping ability to the
full_analysis.py script in the relax repository (to both
the 1.2
and
1.3 lines). This is not activated by default though
and the
scripts
in the repository are significantly different from that in
the
relax
1.2.10 version (all the variables which should be
modified by
the user
have been shifted to the top of the script). Would you be
able to
test if this automatic looping over all rounds of
optimisation
until
convergence actually works? There could possibly be bugs
lurking
there. Thanks.
The problem that you encountered with the calling of the
__init__()
function is because this function should not be called.
Using that
type of approach, the looping should have been outside
of the
Main
class to work.
Cheers,
Edward
On 6/16/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx>
wrote:
Hi All,
Is it possible to edit full_analysis.py so the
optimization of
MII to
MV (self.round > 0) is done automatically by looping
until
convergence?
Do you mean that the script will automatically
I tried to do this by modifying the following in
convergence() [near the end]:
"""
# Final print out.
##################
print "\nConvergence:"
if chi2_converged and models_converged and
params_converged:
print " [ Yes ]"
return 1
else:
print " [ No ]"
return 0
"""
then modifying __init__(), at the end of the "elif
DIFF_MODEL ==
'sphere' or DIFF_MODEL == 'prolate' or DIFF_MODEL ==
'oblate' or
DIFF_MODEL == 'ellipsoid':" statement:
"""
# Test for convergence.
test=self.convergence(run=name)
if test == 0:
__init__(self.relax)
#Main(self.relax)
"""
but it did not work properly. I think the problem has
something to
do with the call to __init__() or Main(). I'll see if
I can
dig up
the error reported by relax.
Thanks,
Doug
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______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
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Re: looping the optimization in full_analysis.py